healthcareio
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parser
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bug fix: export import bug

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dev
Steve Nyemba 2 years ago
parent 995ea21320
commit ddddb897d0
6 changed files with 121 additions and 68 deletions
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72
healthcareio/analytics.py
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@ -192,18 +192,23 @@ class Apex :
@staticmethod @staticmethod
def scalar(item): def scalar(item):
_df = item['data'] _df = item['data']
value = '0'
name = _df.columns.tolist()[0] unit = ''
value = _df[name].values.round(2)[0]
html = '<div class="scalar"><div class="value">:value</div><div class="label">:label</div></div>' html = '<div class="scalar"><div class="value">:value</div><div class="label">:label</div></div>'
if value > 999 and value < 1000000 : if _df.shape[0] > 0 :
value = " ".join([str(np.divide(value,1000).round(2)),"K"]) print (_df)
elif value > 999999 : print ('_____________________________________')
#@ Think of considering the case of a billion ... name = _df.columns.tolist()[0]
value = " ".join([str(np.divide(value,1000000).round(2)),"M"]) value = _df[name].values[0]
else:
value = str(value) if value > 999 and value < 1000000 :
unit = name.replace('_',' ') if 'unit' not in item else item['unit'] value = " ".join([str(np.divide(value,1000).round(2)),"K"])
elif value > 999999 :
#@ Think of considering the case of a billion ...
value = " ".join([str(np.divide(value,1000000).round(2)),"M"])
else:
value = str(value)
unit = name.replace('_',' ') if 'unit' not in item else item['unit']
return {'html':html.replace(':value',value).replace(":label",unit)} return {'html':html.replace(':value',value).replace(":label",unit)}
@staticmethod @staticmethod
def column(item): def column(item):
@ -319,8 +324,9 @@ class Apex :
values = df[x_cols].values.round(2).tolist() values = df[x_cols].values.round(2).tolist()
else: else:
labels = [name.upper().replace('_',' ') for name in df.columns.tolist()] labels = [name.upper().replace('_',' ') for name in df.columns.tolist()]
df = df.astype(float) # df = df.astype(float)
values = df.values.round(2).tolist()[0] if df.shape[1] > 1 else df.values.round(2).tolist() # values = df.values.round(2).tolist()[0] if df.shape[1] > 1 else df.values.round(2).tolist()
values = df[[name for name in df.columns if df[name].dtype in [float,int]] ].values.round(2).tolist()
colors = COLORS[:len(values)] colors = COLORS[:len(values)]
options = {"series":values,"colors":colors,"labels":labels,"dataLabels":{"enabled":True,"style":{"colors":["#000000"]},"dropShadow":{"enabled":False}},"chart":{"type":"donut","width":200},"plotOptions":{"pie":{"customScale":.9}},"legend":{"position":"right"}} options = {"series":values,"colors":colors,"labels":labels,"dataLabels":{"enabled":True,"style":{"colors":["#000000"]},"dropShadow":{"enabled":False}},"chart":{"type":"donut","width":200},"plotOptions":{"pie":{"customScale":.9}},"legend":{"position":"right"}}
@ -343,10 +349,10 @@ class engine :
self.store_config = _config['store'] self.store_config = _config['store']
self.info = _config['analytics'] self.info = _config['analytics']
_args = self.store_config _args = self.store_config
if self.store_config['type'] == 'mongo.MongoWriter' : if 'type' not in self.store_config :
_args['type'] = 'mongo.MongoReader' #
else: # This is the newer version of data-transport
_args['type'] = 'disk.SQLiteReader' self.store_config['context'] = 'read'
self.store_config = _args ; self.store_config = _args ;
def filter (self,**args): def filter (self,**args):
@ -367,8 +373,8 @@ class engine :
# conn = lite.connect(self.store_config['args']['path'],isolation_level=None) # conn = lite.connect(self.store_config['args']['path'],isolation_level=None)
# conn.create_aggregate("stdev",1,stdev) # conn.create_aggregate("stdev",1,stdev)
DB_TYPE = 'mongo' if (type(self.reader) == transport.mongo.MongoReader) else 'sql' DB_TYPE = 'mongo' if (type(self.reader) == transport.mongo.MongoReader) else 'sql'
if DB_TYPE == 'mongo' : # if DB_TYPE == 'mongo' :
self.store_config['args']['doc'] = args['type'] # self.store_config['args']['doc'] = args['type']
self.reader = transport.factory.instance(**self.store_config) self.reader = transport.factory.instance(**self.store_config)
r = [] r = []
@ -414,20 +420,8 @@ class engine :
_analytics = [_analytics[index]] _analytics = [_analytics[index]]
_info = list(_analytics) if 'filter' not in args else [item for item in analytics if args['filter'] == item['id']] _info = list(_analytics) if 'filter' not in args else [item for item in analytics if args['filter'] == item['id']]
# conn = lite.connect(self.store_config['args']['path'],isolation_level=None)
# conn.create_aggregate("stdev",1,stdev)
#
# @TODO: Find a better way to handle database variance
#
# DB_TYPE = 'mongo' if (type(self.reader) == transport.mongo.MongoReader) else 'sql'
if 'mongo' in self.store_config['type'] :
DB_TYPE='mongo'
else:
DB_TYPE='sql'
self.store_config['args']['table'] = args['type']
self.reader = transport.factory.instance(**self.store_config) self.reader = transport.factory.instance(**self.store_config)
DB_TYPE = 'mongo' if self.store_config ['provider'] in ['mongodb','mongo'] else 'sql'
r = [] r = []
for row in _info : for row in _info :
pipeline = row['pipeline'] pipeline = row['pipeline']
@ -440,14 +434,22 @@ class engine :
continue continue
if DB_TYPE == 'sql' : if DB_TYPE == 'sql' :
query = {"sql":query} query = {"sql":query}
else:
query = {DB_TYPE:query}
item['data'] = self.reader.read(**query) #item) _df = self.reader.read(**query) #item)
print (query)
print (self.reader)
if 'serialize' in args : if 'serialize' in args :
# item['data'] = json.dumps(item['data'].to_dict(orient='record')) if type(item['data']) == pd.DataFrame else item['data'] # item['data'] = json.dumps(item['data'].to_dict(orient='record')) if type(item['data']) == pd.DataFrame else item['data']
item['data'] = json.dumps(item['data'].to_dict('record')) if type(item['data']) == pd.DataFrame else item['data'] item['data'] = json.dumps(_df.to_dict(orient='record'))
else: else:
item['data'] = (pd.DataFrame(item['data'])) # item['data'] = (pd.DataFrame(item['data']))
item['data'] = _df
pass
print (_df.head())
break
pipeline[index] = item pipeline[index] = item
index += 1 index += 1
# #

1
healthcareio/server/__init__.py
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@ -225,6 +225,7 @@ if __name__ == '__main__' :
PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json']) PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
# #
# Adjusting configuration with parameters (batch,folder,resume) # Adjusting configuration with parameters (batch,folder,resume)
SYS_ARGS['config'] = json.loads(open(PATH).read())
if 'args' not in SYS_ARGS['config'] : if 'args' not in SYS_ARGS['config'] :
SYS_ARGS['config']["args"] = {"batch":1,"resume":True,"folder":"/data"} SYS_ARGS['config']["args"] = {"batch":1,"resume":True,"folder":"/data"}

16
healthcareio/server/index.py
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@ -6,15 +6,16 @@ import json
app = Flask(__name__) app = Flask(__name__)
@app.route("/favicon.ico") @app.route("/favicon.ico")
def _icon(): def _icon():
return send_from_directory(os.path.join([app.root_path, 'static','img','logo.svg']), return send_from_directory(os.path.join([app.root_path, 'static/img/logo.svg']),
'favicon.ico', mimetype='image/vnd.microsoft.icon') 'favicon.ico', mimetype='image/vnd.microsoft.icon')
@app.route("/") @app.route("/")
def init(): def init():
e = SYS_ARGS['engine'] e = SYS_ARGS['engine']
sections = {"remits":e.info['835'],"claims":e.info['837']} sections = {"remits":e.info['835'],"claims":e.info['837']}
_args = {"sections":sections,"store":SYS_ARGS['config']['store']}
print (SYS_ARGS['config']['store']) _args = {"sections":sections,"store":SYS_ARGS['config']['store'],'args':{'batch':5}}
return render_template("setup.html",**_args)
return render_template("index.html",**_args)
@app.route("/format/<id>/<index>",methods=['POST']) @app.route("/format/<id>/<index>",methods=['POST'])
def _format(id,index): def _format(id,index):
@ -73,13 +74,16 @@ def reload():
if __name__ == '__main__' : if __name__ == '__main__' :
PORT = int(SYS_ARGS['port']) if 'port' in SYS_ARGS else 5500 PORT = int(SYS_ARGS['port']) if 'port' in SYS_ARGS else 5500
DEBUG= int(SYS_ARGS['debug']) if 'debug' in SYS_ARGS else 0 DEBUG= int(SYS_ARGS['debug']) if 'debug' in SYS_ARGS else 1
SYS_ARGS['context'] = SYS_ARGS['context'] if 'context' in SYS_ARGS else '' SYS_ARGS['context'] = SYS_ARGS['context'] if 'context' in SYS_ARGS else ''
# #
# #
PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json']) PATH= SYS_ARGS['config'] if 'config' in SYS_ARGS else os.sep.join([os.environ['HOME'],'.healthcareio','config.json'])
#
if os.path.exists(PATH) :
SYS_ARGS['config'] = json.loads(open(PATH).read())
e = healthcareio.analytics.engine(PATH) e = healthcareio.analytics.engine(PATH)
# e.apply(type='claims',serialize=True) # e.apply(type='claims',serialize=True)
SYS_ARGS['engine'] = e SYS_ARGS['engine'] = e
app.run(host='0.0.0.0',port=PORT,debug=DEBUG,threaded=True) app.run(host='0.0.0.0',port=PORT,debug=DEBUG,threaded=True)

46
healthcareio/server/proxy.py
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@ -37,14 +37,17 @@ class get :
@staticmethod @staticmethod
def processes(_args): def processes(_args):
_info = pd.DataFrame(smart.top.read(name='healthcare-io.py'))[['name','cpu','mem']] APP_NAME ='healthcare-io'
_info = smart.top.read(name=APP_NAME) #pd.DataFrame(smart.top.read(name='healthcare-io'))[['name','cpu','mem']]
if _info.shape[0] == 0 : if _info.shape[0] == 0 :
_info = pd.DataFrame({"name":["healthcare-io.py"],"cpu":[0],"mem":[0]}) _info = pd.DataFrame({"name":[APP_NAME],"cpu":[0],"mem":[0]})
# _info = pd.DataFrame(_info.groupby(['name']).sum()) # _info = pd.DataFrame(_info.groupby(['name']).sum())
# _info['name'] = ['healthcare-io.py'] # _info['name'] = ['healthcare-io.py']
m = {'cpu':'CPU','mem':'RAM','name':'name'} m = {'cpu':'CPU','mem':'RAM','name':'name'}
_info.columns = [m[name] for name in _info.columns.tolist()] _info = _info.rename(columns=m)
# _info.columns = [m[name] for name in _info.columns.tolist() if name in m]
_info.index = np.arange(_info.shape[0]) _info.index = np.arange(_info.shape[0])
charts = [] charts = []
@ -56,23 +59,20 @@ class get :
{"data":df, "chart":{"type":"radial","axis":{"x":label,"y":"name"}}} {"data":df, "chart":{"type":"radial","axis":{"x":label,"y":"name"}}}
)['apex'] )['apex']
) )
#
# This will update the counts for the processes, upon subsequent requests so as to show the change return {"process":{"chart":charts,"counts":_info.shape[0]}}
#
N = 0
lprocs = []
for proc in get.PROCS :
if proc.is_alive() :
lprocs.append(proc)
N = len(lprocs)
get.PROCS = lprocs
return {"process":{"chart":charts,"counts":N}}
@staticmethod @staticmethod
def files (_args): def files (_args):
_info = smart.folder.read(path='/data') folder = _args['args']['folder']
_info = smart.folder.read(path=folder)
N = _info.files.tolist()[0] N = _info.files.tolist()[0]
if 'mongo' in _args['store']['type'] : store_args = _args['store'].copy()
store_args = dict(_args['store'].copy(),**{"type":"mongo.MongoReader"}) store_args['context'] = 'read'
# if 'mongo' in _args['store']['type'] :
if _args['store']['provider'] in ['mongo', 'mongodb']:
# store_args = dict(_args['store'].copy(),**{"type":"mongo.MongoReader"})
# reader = transport.factory.instance(**_args) # reader = transport.factory.instance(**_args)
pipeline = [{"$group":{"_id":"$name","count":{"$sum":{"$cond":[{"$eq":["$completed",True]},1,0]}} }},{"$group":{"_id":None,"count":{"$sum":"$count"}}},{"$project":{"_id":0,"status":"completed","count":1}}] pipeline = [{"$group":{"_id":"$name","count":{"$sum":{"$cond":[{"$eq":["$completed",True]},1,0]}} }},{"$group":{"_id":None,"count":{"$sum":"$count"}}},{"$project":{"_id":0,"status":"completed","count":1}}]
@ -83,12 +83,15 @@ class get :
else: else:
store_args = dict(_args['store'].copy(),**{"type":"disk.SQLiteReader"}) # store_args = dict(_args['store'].copy(),**{"type":"disk.SQLiteReader"})
store_args['args']['table'] = 'logs'
# store_args['args']['table'] = 'logs'
store_args['table'] = 'logs'
query= {"sql":"select count(distinct json_extract(data,'$.name')) as count, 'completed' status from logs where json_extract(data,'$.completed') = true"} query= {"sql":"select count(distinct json_extract(data,'$.name')) as count, 'completed' status from logs where json_extract(data,'$.completed') = true"}
_query={"sql":"select json_extract(data,'$.parse') as type,count(distinct json_extract(data,'$.name')) as count from logs group by type"} #-- distribution claim/remits _query={"sql":"select json_extract(data,'$.parse') as type,count(distinct json_extract(data,'$.name')) as count from logs group by type"} #-- distribution claim/remits
reader = transport.factory.instance(**store_args) reader = transport.factory.instance(**store_args)
_info = pd.DataFrame(reader.read(**query)) _info = pd.DataFrame(reader.read(**query))
if not _info.shape[0] : if not _info.shape[0] :
_info = pd.DataFrame({"status":["completed"],"count":[0]}) _info = pd.DataFrame({"status":["completed"],"count":[0]})
_info['count'] = np.round( (_info['count'] * 100 )/N,2) _info['count'] = np.round( (_info['count'] * 100 )/N,2)
@ -97,11 +100,6 @@ class get :
# #
# Let us classify the files now i.e claims / remits # Let us classify the files now i.e claims / remits
# #
# pipeline = [{"$group":{"_id":"$parse","claims":{"$addToSet":"$name"}}},{"$project":{"_id":0,"type":"$_id","count":{"$size":"$claims"}}}]
# _args = {"aggregate":"logs","cursor":{},"allowDiskUse":True,"pipeline":pipeline}
# r = pd.DataFrame(reader.read(mongo=_args))
r = pd.DataFrame(reader.read(**_query)) #-- distribution claims/remits r = pd.DataFrame(reader.read(**_query)) #-- distribution claims/remits
r = Apex.apply({"chart":{"type":"donut","axis":{"x":"count","y":"type"}},"data":r})['apex'] r = Apex.apply({"chart":{"type":"donut","axis":{"x":"count","y":"type"}},"data":r})['apex']
r['chart']['height'] = '100%' r['chart']['height'] = '100%'

4
healthcareio/server/templates/setup.html
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@ -63,10 +63,10 @@
// //
// We should insure the listeners are enabled // We should insure the listeners are enabled
if(monitor.listen.handler == null){ if(monitor.listen.handler == null){
monitor.listen.handler = setInterval( /*monitor.listen.handler = setInterval(
function(){ function(){
console.log('running ...') console.log('running ...')
monitor.data()},5000) monitor.data()},5000)*/
} }
}else{ }else{

50
healthcareio/x12/__init__.py
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@ -24,6 +24,7 @@ import sys
from itertools import islice from itertools import islice
from multiprocessing import Process from multiprocessing import Process
import transport import transport
from transport import providers
import jsonmerge import jsonmerge
import copy import copy
@ -236,7 +237,54 @@ class Parser (Process):
_config[_id] = [_config[_id]] _config[_id] = [_config[_id]]
config['parser'] = _config config['parser'] = _config
return config return config
@staticmethod
def init(**_args):
"""
This function allows to initialize the database that will store the claims if need be
:path configuration file
"""
PATH = os.sep.join([os.environ['HOME'],'.healthcareio'])
filename = os.sep.join([PATH,'config.json'])
filename = _args['path'] if 'path' in _args else filename
info = None
if os.path.exists(filename):
#
# Loading the configuration file (JSON format)
file = open(filename)
info = json.loads(file.read())
OUTPUT_FOLDER = info['out-folder']
if 'output-folder' not in info and not os.path.exists(OUTPUT_FOLDER) :
os.mkdir(OUTPUT_FOLDER)
elif 'output-folder' in info and not os.path.exists(info['out-folder']) :
os.mkdir(info['out-folder'])
# if 'type' in info['store'] :
lwriter = None
IS_SQL = False
if'type' in info['store'] and info['store']['type'] == 'disk.SQLiteWriter' :
lwriter = transport.factory.instance(**info['store'])
IS_SQL = True
elif 'provider' in info['store'] and info['store']['provider'] == 'sqlite' :
lwriter = transport.instance(**info['store']) ;
IS_SQL = [providers.SQLITE,providers.POSTGRESQL,providers.NETEZZA,providers.MYSQL,providers.MARIADB]
if lwriter and IS_SQL:
for key in info['schema'] :
if key != 'logs' :
_id = 'claims' if key == '837' else 'remits'
else:
_id = key
if not lwriter.has(table=_id) :
lwriter.apply(info['schema'][key]['create'])
# [lwriter.apply( info['schema'][key]['create']) for key in info['schema'] if not lwriter.has(table=key)]
lwriter.close()
return info
def __init__(self,path): def __init__(self,path):
""" """
:path path of the configuration file (it can be absolute) :path path of the configuration file (it can be absolute)

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